| Department of Computer Science
|University of Toronto
In September 2004 I finished a M.Sc. in the Database Group of
the Department of
Computer Science at the University of Toronto,
although most of my work was with the Machine Learning
Group. I started this M.Sc. in September 2002 under the
supervision of Anthony
Bonner. My master's thesis dealt with data mining and pattern recognition
in a particular case of datasets with very few positive samples. I worked on
a bioinformatics application: statistical
learning of gene annotations in Saccharomyces
From September 2003 to February 2005, I was also working in Hughes' Lab at the
Best Institute doing analysis and processing of biological data. My main activities
were database development, statistical analysis, and software development.
Research, Publications & Projects
- Detection and discovery of RNA modifications using microarrays.
Shawna L. Hiley, Jane Jackman, Tomas Babak, Miles Trochesset, Quaid D. Morris, Eric Phizicky, and Timothy R. Hughes
Nucleic Acids Research 2005 Jan 7;33(1):e2
HTML - PDF
- Statistical Learning of Gene Annotations in Saccharomyces Cerevisiae
M.Sc. Thesis, Department of Computer Science, University of Toronto. Sept 2004.
PDF - PS
- Clustering Labeled Data and Cross-Validation for Classification with Few Positives in Yeast
Miles Trochesset and Anthony Bonner.
In Proceedings of the 4th ACM SIGKDD Workshop on Data Mining in Bioinformatics (BioKDD) at
KDD 2004, Seattle, WA, USA, August 22-25, 2004.
PDF - PS
- Exploration of Essential Gene Functions Via Titratable Promoter Alleles
Cell 2004 July 9;118(1):31-44.
- A Global View of Yeast Noncoding RNA, Processing and Modification
Shawna Hiley, Miles Trochesset, Quaid Morris, Tomas Babak and Tim Hughes
RNA 2004 (9th Annual Meeting of the RNA Society), University of Wisconsin, Madison, June 1-6 2004.
Yeast 2004 (Yeast Genetics and Molecular Biology Meeting), University of Washington, Seattle, July 27 - August 1st 2004.
- Microarray analysis and normalization.
Statistical techniques, software development for custom arrays.
- Design of 60-mer oligonucleotides for whole-genome analysis of Fugu Rubripes, Tetraodon, Saccharomyces cerevisiae, Mus musculus, Gallus gallus and Xenopus tropicalis.
- Building a non redundant list of all known and predicted Mouse genes.
Work done in common with Mark Robinson.
Involves querying MGI, GenBank, RefSeq, Novartis, EnsEMBL, UniGene, GeneID etc. and mapping
all hits to the Mouse chromosomes (Build 32) to detect redundancy.
Miles Trochesset, Database Group, UofT Dept. of Computer Science || www.cs.toronto.edu/~mtroches
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